You should adjust the water depth or your skimmer so that you can skim.
Was your skimmer fine before adding biopellets?
The reason you should skim while running biopellets (or doing any form of carbon dosing, of which biopellets are a form of carbon dosing), is that biopellets only feed carbon to bacteria in the tank, which allows them to grow, consuming carbon, nitrate, and phosphate. If you aren't removing them either through skimming or big frequent water changes, then they're not going anywhere, and will just break down in the tank, leaving the nitrate and phosphate waste in the water as it was before.
If they're not skimmed out, you can think of your nitrates and phosphate levels looking like an upside-down normal distribution curve. The levels drop, but because the bacteria aren't removed, and then they die, the levels just go right back up again to where they were before (though actually could go higher since background levels stayed the same).
So if you're not skimming, or physically removing the bacteria from the tank, you shouldn't carbon dose (including biopellets).
You can turn off the reactor for a while, and the majority of the bacteria will die, which could increase nutrient levels slightly, but hopefully not too much unless it's a very large reactor.
